Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012217.1 Kokia drynarioides strain JFW-HI SEQ_127218, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 11638
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:1679 original size:18 final size:18

Alignment explanation


    Indices: 1652--1686  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1642 ATATATGAAA

                              
       1652 ATGACATAAATAGTTGAG
          1 ATGACATAAATAGTTGAG

                 *     *     
       1670 ATGACTTAAATGGTTGA
          1 ATGACATAAATAGTTGA

       1687 ACTTGTCTAT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31


Consensus pattern (18 bp):   
ATGACATAAATAGTTGAG

Found at i:3833 original size:24 final size:24

Alignment explanation


    Indices: 3805--3855  Score: 84
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       3795 AGAAACAATC

                 *                  
       3805 TTTCAGTTAAACTCTGTTTAATTG
          1 TTTCAATTAAACTCTGTTTAATTG

                                *   
       3829 TTTCAATTAAACTCTGTTTATTTG
          1 TTTCAATTAAACTCTGTTTAATTG

               
       3853 TTT
          1 TTT

       3856 GAGCCAAACT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55


Consensus pattern (24 bp):   
TTTCAATTAAACTCTGTTTAATTG

Found at i:3864 original size:24 final size:24

Alignment explanation


    Indices: 3813--3867  Score: 65
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       3803 TCTTTCAGTT

                                  **
       3813 AAACTCTGTTTAATTGTTTCAATT
          1 AAACTCTGTTTAATTGTTTCAACC

                        *      * *  
       3837 AAACTCTGTTTATTTGTTTGAGCC
          1 AAACTCTGTTTAATTGTTTCAACC

                   
       3861 AAACTCT
          1 AAACTCT

       3868 TATTAGTCTA


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45


Consensus pattern (24 bp):   
AAACTCTGTTTAATTGTTTCAACC

Found at i:5870 original size:22 final size:22

Alignment explanation


    Indices: 5832--5897  Score: 78
    Period size: 22  Copynumber: 3.0  Consensus size: 22

       5822 CTCTGATTAT

                                   
       5832 TTAGCACATATTGTGCTCTCCGA
          1 TTAGCACAT-TTGTGCTCTCCGA

                   *             *
       5855 TTAGCACGTTTGTGCTCTCCGT
          1 TTAGCACATTTGTGCTCTCCGA

                   ***           
       5877 TTAGCACCCCTGTGCTCTCCG
          1 TTAGCACATTTGTGCTCTCCG

       5898 TTTATTTGTG


Statistics
Matches: 38,  Mismatches: 5, Indels: 1
        0.86            0.11        0.02

Matches are distributed among these distances:
  22   30  0.79
  23    8  0.21

ACGTcount: A:0.14, C:0.32, G:0.20, T:0.35


Consensus pattern (22 bp):   
TTAGCACATTTGTGCTCTCCGA

Found at i:5898 original size:22 final size:22

Alignment explanation


    Indices: 5843--5901  Score: 82
    Period size: 22  Copynumber: 2.7  Consensus size: 22

       5833 TAGCACATAT

                       *       ***
       5843 TGTGCTCTCCGATTAGCACGTT
          1 TGTGCTCTCCGTTTAGCACCCC

                                  
       5865 TGTGCTCTCCGTTTAGCACCCC
          1 TGTGCTCTCCGTTTAGCACCCC

                           
       5887 TGTGCTCTCCGTTTA
          1 TGTGCTCTCCGTTTA

       5902 TTTGTGCATT


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  22   33  1.00

ACGTcount: A:0.10, C:0.32, G:0.20, T:0.37


Consensus pattern (22 bp):   
TGTGCTCTCCGTTTAGCACCCC
Done.